Dataset Information

Virus Metagenomics in Farm Animals: A Systematic Review.

ABSTRACT: A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the "FAIR" (Findable, Accessible, Interoperable, and Reusable) data principles.

SUBMITTER: Kwok KTT

PROVIDER: S-EPMC7019290 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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Virus Metagenomics in Farm Animals: A Systematic Review.

Kwok Kirsty T T KTT Nieuwenhuijse David F DF Phan My V T MVT Koopmans Marion P G MPG

Viruses 20200116 1

A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. P ...[more]

PMID: 31963174

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Project description:The emergence and spread of antibiotic resistance is a growing global threat and has aroused a global interest in limiting antibiotic use in animal agriculture. As we are entering the post-antibiotic era, there is a growing need for identifying alternatives to antibiotics for prevention and treatment. Although phytotherapeutic remedies are available and are used in Europe, evidence of their efficacy is currently very limited but is nevertheless still necessary. A systematic review of phytotherapy used for the treatment and prevention of infectious diseases in farm animals has been conducted using the PICOS approach. Analysis and extraction of information from studies was performed according to a protocol, and included: publication year and source, research body, species, farming system, purpose of application, disease in focus, diagnostic method, remedy used (origin and ingredients of the remedy), producer of remedy, way of administration, study design, and control groups, measure of effect, and outcome of the study. A total of 1,705 papers were screened, but only 44 (comprising 53 independent studies) met the inclusion criteria. The majority of the scientific studies identified show limitations in the study design as well as in presentation and standardization of the botanical remedies studied, which limits the possibilities of drawing firm conclusions. Preventive effect was investigated in 89% of the studies. Half of the studies reported uncertain effects of the botanical remedies on subclinical measures in comparison to a control group. The review highlights unresolved questions such as the need for standardized controlled trials and for improved standardization of the botanical products by analytical methods, such as high-performance liquid chromatography. It is necessary to consider this in order to achieve replicable outcomes and establish efficacy and safety of phytotherapy in farm practice. The manageability of alternative medicine in farm animals also warrants further investigation so as to ascertain whether all necessary preconditions for their use are being granted.

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Dataset Information

Virus Metagenomics in Farm Animals: A Systematic Review.

Publications

Virus Metagenomics in Farm Animals: A Systematic Review.

Similar Datasets

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